Preliminary data exploration
Contaminant ASVs were identified with the prevalence method using the decontam package.
Plant measures overview
Scaled-centered plant ‘health’ measures, broken down by treatment factors.
Model output
Formula:value ~ drought * host * site + (1|block))
| effect | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|
| fixed | (Intercept) | 0.071 | 0.280 | 0.255 | 5.343 | 0.808 |
| fixed | droughtND | -0.017 | 0.163 | -0.106 | 384.262 | 0.916 |
| fixed | hostCeanothus velutinus | -0.522 | 0.164 | -3.190 | 381.647 | 0.002 |
| fixed | fire_freq | 0.104 | 0.154 | 0.675 | 5.360 | 0.528 |
| fixed | droughtND:hostCeanothus velutinus | 0.560 | 0.232 | 2.412 | 383.262 | 0.016 |
| fixed | droughtND:fire_freq | -0.037 | 0.089 | -0.416 | 381.323 | 0.677 |
| fixed | hostCeanothus velutinus:fire_freq | -0.002 | 0.090 | -0.017 | 382.464 | 0.987 |
| fixed | droughtND:hostCeanothus velutinus:fire_freq | -0.033 | 0.127 | -0.263 | 382.083 | 0.793 |
Inoculum communities overview
Taxonomic overview
Bacteria
Alpha diversity
Effect of Shannon diversity on plant measures
## overall_transformed_plant_value ~ Shannon * host * drought *
## inoculum_site + (1 | block)
## <environment: 0x5601b01369d0>| effect | group | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|---|
| fixed | NA | (Intercept) | -0.819 | 0.484 | -1.694 | 268.342 | 0.091 |
| fixed | NA | Shannon | 0.177 | 0.100 | 1.775 | 780.109 | 0.076 |
| fixed | NA | hostCeanothus velutinus | 2.273 | 2.532 | 0.898 | 780.696 | 0.369 |
| fixed | NA | droughtND | 0.046 | 2.327 | 0.020 | 779.536 | 0.984 |
| fixed | NA | inoculum_site2 | 0.456 | 1.895 | 0.241 | 780.321 | 0.810 |
| fixed | NA | inoculum_site3 | 1.569 | 4.454 | 0.352 | 780.682 | 0.725 |
| fixed | NA | inoculum_site4 | 1.462 | 1.848 | 0.791 | 780.526 | 0.429 |
| fixed | NA | inoculum_site5 | 4.449 | 3.412 | 1.304 | 780.446 | 0.193 |
| fixed | NA | inoculum_site6 | 4.364 | 1.829 | 2.386 | 781.163 | 0.017 |
| fixed | NA | inoculum_siteSterile | 4.004 | 2.605 | 1.537 | 780.352 | 0.125 |
| fixed | NA | Shannon:hostCeanothus velutinus | -0.400 | 0.419 | -0.953 | 780.740 | 0.341 |
| fixed | NA | Shannon:droughtND | -0.051 | 0.404 | -0.126 | 779.252 | 0.900 |
| fixed | NA | hostCeanothus velutinus:droughtND | 10.860 | 8.385 | 1.295 | 782.221 | 0.196 |
| fixed | NA | Shannon:inoculum_site2 | -0.052 | 0.342 | -0.152 | 780.485 | 0.879 |
| fixed | NA | Shannon:inoculum_site3 | -0.387 | 0.746 | -0.520 | 780.705 | 0.603 |
| fixed | NA | Shannon:inoculum_site4 | -0.245 | 0.349 | -0.703 | 780.601 | 0.482 |
| fixed | NA | Shannon:inoculum_site5 | -0.748 | 0.606 | -1.236 | 780.466 | 0.217 |
| fixed | NA | Shannon:inoculum_site6 | -0.756 | 0.326 | -2.318 | 781.337 | 0.021 |
| fixed | NA | Shannon:inoculum_siteSterile | -0.776 | 0.452 | -1.717 | 780.449 | 0.086 |
| fixed | NA | hostCeanothus velutinus:inoculum_site2 | -1.587 | 3.204 | -0.495 | 781.728 | 0.621 |
| fixed | NA | hostCeanothus velutinus:inoculum_site3 | -4.607 | 6.361 | -0.724 | 782.858 | 0.469 |
| fixed | NA | hostCeanothus velutinus:inoculum_site4 | -7.546 | 4.486 | -1.682 | 781.379 | 0.093 |
| fixed | NA | hostCeanothus velutinus:inoculum_site5 | -10.835 | 6.908 | -1.569 | 780.616 | 0.117 |
| fixed | NA | hostCeanothus velutinus:inoculum_site6 | -20.126 | 7.710 | -2.610 | 778.552 | 0.009 |
| fixed | NA | hostCeanothus velutinus:inoculum_siteSterile | -4.124 | 4.378 | -0.942 | 782.874 | 0.347 |
| fixed | NA | droughtND:inoculum_site2 | -0.849 | 3.219 | -0.264 | 777.976 | 0.792 |
| fixed | NA | droughtND:inoculum_site3 | 0.110 | 5.737 | 0.019 | 783.218 | 0.985 |
| fixed | NA | droughtND:inoculum_site4 | 0.927 | 3.782 | 0.245 | 780.024 | 0.806 |
| fixed | NA | droughtND:inoculum_site5 | -2.156 | 4.458 | -0.484 | 779.469 | 0.629 |
| fixed | NA | droughtND:inoculum_site6 | -2.233 | 3.776 | -0.591 | 779.727 | 0.555 |
| fixed | NA | droughtND:inoculum_siteSterile | -2.731 | 4.482 | -0.609 | 778.655 | 0.542 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND | -1.855 | 1.431 | -1.296 | 782.184 | 0.195 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site2 | 0.244 | 0.545 | 0.448 | 781.808 | 0.655 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site3 | 0.799 | 1.031 | 0.775 | 782.885 | 0.438 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site4 | 1.299 | 0.756 | 1.719 | 781.400 | 0.086 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site5 | 1.841 | 1.136 | 1.620 | 780.686 | 0.106 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site6 | 3.330 | 1.240 | 2.685 | 778.493 | 0.007 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_siteSterile | 0.796 | 0.731 | 1.090 | 782.862 | 0.276 |
| fixed | NA | Shannon:droughtND:inoculum_site2 | 0.174 | 0.570 | 0.305 | 777.990 | 0.761 |
| fixed | NA | Shannon:droughtND:inoculum_site3 | -0.024 | 0.977 | -0.025 | 781.714 | 0.980 |
| fixed | NA | Shannon:droughtND:inoculum_site4 | -0.044 | 0.665 | -0.066 | 779.789 | 0.947 |
| fixed | NA | Shannon:droughtND:inoculum_site5 | 0.395 | 0.787 | 0.502 | 779.396 | 0.616 |
| fixed | NA | Shannon:droughtND:inoculum_site6 | 0.418 | 0.678 | 0.617 | 779.658 | 0.538 |
| fixed | NA | Shannon:droughtND:inoculum_siteSterile | 0.554 | 0.771 | 0.719 | 778.585 | 0.473 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site2 | -8.856 | 8.911 | -0.994 | 781.979 | 0.321 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site3 | -13.316 | 11.036 | -1.207 | 783.994 | 0.228 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site4 | -5.064 | 9.701 | -0.522 | 781.885 | 0.602 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site5 | -0.503 | 11.503 | -0.044 | 779.167 | 0.965 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site6 | 9.731 | 11.483 | 0.847 | 778.849 | 0.397 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_siteSterile | -8.440 | 9.784 | -0.863 | 780.605 | 0.389 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 | 1.523 | 1.530 | 0.996 | 781.901 | 0.320 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 | 2.324 | 1.858 | 1.251 | 783.936 | 0.211 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 | 0.760 | 1.660 | 0.458 | 781.800 | 0.647 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 | 0.143 | 1.924 | 0.074 | 779.246 | 0.941 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 | -1.561 | 1.918 | -0.814 | 778.858 | 0.416 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile | 1.366 | 1.666 | 0.820 | 780.518 | 0.413 |
| ran_pars | block | sd__(Intercept) | 0.400 | NA | NA | NA | NA |
| ran_pars | Residual | sd__Observation | 0.898 | NA | NA | NA | NA |
Fungi
Alpha diversity
Effect of Shannon diversity on plant measures
## overall_transformed_plant_value ~ Shannon * host * drought *
## inoculum_site + (1 | block)
## <environment: 0x5601b01369d0>| effect | group | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|---|
| fixed | NA | (Intercept) | 0.188 | 0.339 | 0.555 | 61.518 | 0.581 |
| fixed | NA | Shannon | -0.217 | 0.217 | -0.998 | 780.047 | 0.319 |
| fixed | NA | hostCeanothus velutinus | -0.461 | 0.737 | -0.626 | 779.946 | 0.532 |
| fixed | NA | droughtND | -0.282 | 0.608 | -0.463 | 778.006 | 0.643 |
| fixed | NA | inoculum_site2 | 0.040 | 0.603 | 0.066 | 779.498 | 0.947 |
| fixed | NA | inoculum_site3 | -1.247 | 0.968 | -1.289 | 779.884 | 0.198 |
| fixed | NA | inoculum_site4 | 0.302 | 0.389 | 0.776 | 778.100 | 0.438 |
| fixed | NA | inoculum_site5 | -0.513 | 0.798 | -0.644 | 780.535 | 0.520 |
| fixed | NA | inoculum_site6 | 1.255 | 0.763 | 1.646 | 778.880 | 0.100 |
| fixed | NA | inoculum_siteSterile | -0.937 | 0.688 | -1.363 | 779.073 | 0.173 |
| fixed | NA | Shannon:hostCeanothus velutinus | 0.504 | 0.547 | 0.920 | 780.313 | 0.358 |
| fixed | NA | Shannon:droughtND | 0.276 | 0.560 | 0.492 | 778.364 | 0.623 |
| fixed | NA | hostCeanothus velutinus:droughtND | 1.080 | 1.006 | 1.074 | 777.445 | 0.283 |
| fixed | NA | Shannon:inoculum_site2 | 0.312 | 0.458 | 0.681 | 779.891 | 0.496 |
| fixed | NA | Shannon:inoculum_site3 | 0.579 | 0.631 | 0.917 | 780.107 | 0.359 |
| fixed | NA | Shannon:inoculum_site4 | -0.154 | 0.428 | -0.361 | 778.880 | 0.718 |
| fixed | NA | Shannon:inoculum_site5 | 0.826 | 0.639 | 1.291 | 780.850 | 0.197 |
| fixed | NA | Shannon:inoculum_site6 | -0.702 | 0.574 | -1.224 | 778.945 | 0.221 |
| fixed | NA | Shannon:inoculum_siteSterile | 0.623 | 0.570 | 1.093 | 779.313 | 0.275 |
| fixed | NA | hostCeanothus velutinus:inoculum_site2 | 0.188 | 1.381 | 0.136 | 780.881 | 0.891 |
| fixed | NA | hostCeanothus velutinus:inoculum_site3 | 2.063 | 1.320 | 1.563 | 780.565 | 0.118 |
| fixed | NA | hostCeanothus velutinus:inoculum_site4 | 1.493 | 1.172 | 1.274 | 779.843 | 0.203 |
| fixed | NA | hostCeanothus velutinus:inoculum_site5 | 0.547 | 1.865 | 0.293 | 779.833 | 0.769 |
| fixed | NA | hostCeanothus velutinus:inoculum_site6 | -0.222 | 1.821 | -0.122 | 779.773 | 0.903 |
| fixed | NA | hostCeanothus velutinus:inoculum_siteSterile | 2.113 | 1.538 | 1.374 | 779.727 | 0.170 |
| fixed | NA | droughtND:inoculum_site2 | 0.026 | 0.874 | 0.029 | 778.029 | 0.977 |
| fixed | NA | droughtND:inoculum_site3 | 0.053 | 1.385 | 0.038 | 754.104 | 0.970 |
| fixed | NA | droughtND:inoculum_site4 | 0.236 | 0.748 | 0.315 | 778.469 | 0.753 |
| fixed | NA | droughtND:inoculum_site5 | 1.296 | 1.213 | 1.068 | 779.489 | 0.286 |
| fixed | NA | droughtND:inoculum_site6 | -1.108 | 0.989 | -1.121 | 779.728 | 0.263 |
| fixed | NA | droughtND:inoculum_siteSterile | -0.112 | 1.154 | -0.097 | 778.270 | 0.922 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND | -0.998 | 0.805 | -1.240 | 777.461 | 0.215 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site2 | -0.480 | 0.894 | -0.537 | 781.152 | 0.592 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site3 | -1.443 | 0.887 | -1.626 | 780.757 | 0.104 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site4 | -0.867 | 0.880 | -0.985 | 780.238 | 0.325 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site5 | -0.742 | 1.097 | -0.676 | 780.232 | 0.499 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site6 | 0.261 | 1.054 | 0.247 | 779.406 | 0.805 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_siteSterile | -1.493 | 1.147 | -1.301 | 779.750 | 0.194 |
| fixed | NA | Shannon:droughtND:inoculum_site2 | -0.129 | 0.784 | -0.165 | 778.228 | 0.869 |
| fixed | NA | Shannon:droughtND:inoculum_site3 | -0.260 | 0.969 | -0.268 | 779.728 | 0.788 |
| fixed | NA | Shannon:droughtND:inoculum_site4 | 0.842 | 1.185 | 0.711 | 779.327 | 0.478 |
| fixed | NA | Shannon:droughtND:inoculum_site5 | -1.298 | 1.093 | -1.187 | 779.513 | 0.235 |
| fixed | NA | Shannon:droughtND:inoculum_site6 | 0.823 | 0.821 | 1.002 | 780.023 | 0.317 |
| fixed | NA | Shannon:droughtND:inoculum_siteSterile | 0.408 | 1.067 | 0.382 | 778.550 | 0.702 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site2 | -0.025 | 1.705 | -0.015 | 778.987 | 0.988 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site3 | -1.531 | 1.746 | -0.877 | 776.619 | 0.381 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site4 | -2.530 | 1.433 | -1.765 | 779.634 | 0.078 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site5 | -1.896 | 2.208 | -0.859 | 780.252 | 0.391 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site6 | -0.306 | 2.078 | -0.147 | 778.371 | 0.883 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_siteSterile | -2.291 | 1.949 | -1.176 | 778.956 | 0.240 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 | 0.254 | 1.255 | 0.203 | 778.785 | 0.840 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 | 1.337 | 1.214 | 1.101 | 783.668 | 0.271 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 | 0.768 | 1.459 | 0.526 | 779.898 | 0.599 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 | 1.893 | 1.551 | 1.221 | 780.466 | 0.223 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 | -0.172 | 1.317 | -0.130 | 777.754 | 0.896 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile | 1.751 | 1.668 | 1.050 | 779.048 | 0.294 |
| ran_pars | block | sd__(Intercept) | 0.438 | NA | NA | NA | NA |
| ran_pars | Residual | sd__Observation | 0.902 | NA | NA | NA | NA |
AMF
Alpha diversity
Effect of Shannon diversity on plant measures
## overall_transformed_plant_value ~ Shannon * host * drought *
## inoculum_site + (1 | block)
## <environment: 0x5601b01369d0>| effect | group | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|---|
| fixed | NA | (Intercept) | -0.144 | 0.248 | -0.579 | 135.718 | 0.564 |
| fixed | NA | Shannon | 0.097 | 0.171 | 0.569 | 284.111 | 0.570 |
| fixed | NA | droughtND | -0.188 | 0.369 | -0.509 | 337.141 | 0.611 |
| fixed | NA | inoculum_site1 | -0.014 | 0.458 | -0.031 | 341.818 | 0.975 |
| fixed | NA | inoculum_site2 | 0.000 | 0.658 | 0.000 | 281.993 | 1.000 |
| fixed | NA | inoculum_site3 | -1.135 | 0.494 | -2.297 | 331.577 | 0.022 |
| fixed | NA | inoculum_site4 | 0.505 | 0.357 | 1.415 | 294.169 | 0.158 |
| fixed | NA | inoculum_site5 | -0.089 | 0.617 | -0.143 | 338.737 | 0.886 |
| fixed | NA | inoculum_site6 | 0.665 | 0.565 | 1.177 | 334.193 | 0.240 |
| fixed | NA | Shannon:droughtND | -0.001 | 0.238 | -0.004 | 305.542 | 0.997 |
| fixed | NA | Shannon:inoculum_site1 | 0.052 | 0.283 | 0.183 | 342.000 | 0.855 |
| fixed | NA | Shannon:inoculum_site2 | 0.109 | 0.324 | 0.337 | 234.877 | 0.737 |
| fixed | NA | Shannon:inoculum_site3 | -0.047 | 0.276 | -0.172 | 310.337 | 0.864 |
| fixed | NA | Shannon:inoculum_site4 | -0.122 | 0.250 | -0.488 | 193.801 | 0.626 |
| fixed | NA | Shannon:inoculum_site5 | 0.276 | 0.344 | 0.803 | 341.833 | 0.422 |
| fixed | NA | Shannon:inoculum_site6 | -0.251 | 0.315 | -0.797 | 314.869 | 0.426 |
| fixed | NA | droughtND:inoculum_site1 | 0.497 | 0.689 | 0.721 | 330.092 | 0.472 |
| fixed | NA | droughtND:inoculum_site2 | 0.534 | 1.100 | 0.485 | 268.573 | 0.628 |
| fixed | NA | droughtND:inoculum_site3 | 0.294 | 0.628 | 0.468 | 327.612 | 0.640 |
| fixed | NA | droughtND:inoculum_site4 | -0.451 | 0.619 | -0.729 | 313.535 | 0.467 |
| fixed | NA | droughtND:inoculum_site5 | 1.476 | 1.319 | 1.119 | 298.718 | 0.264 |
| fixed | NA | droughtND:inoculum_site6 | -1.149 | 0.781 | -1.470 | 335.103 | 0.142 |
| fixed | NA | Shannon:droughtND:inoculum_site1 | -0.264 | 0.381 | -0.693 | 320.169 | 0.489 |
| fixed | NA | Shannon:droughtND:inoculum_site2 | -0.255 | 0.479 | -0.533 | 263.141 | 0.595 |
| fixed | NA | Shannon:droughtND:inoculum_site3 | 0.339 | 0.360 | 0.941 | 294.957 | 0.348 |
| fixed | NA | Shannon:droughtND:inoculum_site4 | 0.197 | 0.363 | 0.542 | 256.625 | 0.588 |
| fixed | NA | Shannon:droughtND:inoculum_site5 | -0.779 | 0.589 | -1.322 | 318.767 | 0.187 |
| fixed | NA | Shannon:droughtND:inoculum_site6 | 0.487 | 0.414 | 1.178 | 319.987 | 0.240 |
| ran_pars | block | sd__(Intercept) | 0.158 | NA | NA | NA | NA |
| ran_pars | Residual | sd__Observation | 0.943 | NA | NA | NA | NA |
Comparison between inoculum and root communities
Bacteria
Not all taxa in the inoculae were subsequently found in the root samples
Fungi
Not all taxa in the inoculae were subsequently found in
the root samples
AMF
Not all taxa in the inoculae were subsequently found in the
root samples
Microbial guilds
Bacteria
I couldn’t get a trustworthy annotation of “mutualists” for bacteria, but here are probable pathogens:
## value ~ proportion_pathogen * drought * inoculum_site + (1 |
## block)
## <environment: 0x5601ba2fa7c0>| effect | term | estimate | std.error | statistic | df | p.value | species |
|---|---|---|---|---|---|---|---|
| fixed | (Intercept) | 0.1722 | 0.6500 | 0.2649 | 333.5563 | 0.7913 | Ceanothus |
| fixed | proportion_pathogen | -2.5700 | 1.9957 | -1.2878 | 457.3536 | 0.1985 | Ceanothus |
| fixed | droughtND | -0.5303 | 1.0579 | -0.5013 | 455.0687 | 0.6164 | Ceanothus |
| fixed | inoculum_site2 | -0.0868 | 0.7026 | -0.1235 | 454.5472 | 0.9017 | Ceanothus |
| fixed | inoculum_site3 | -0.7702 | 1.0053 | -0.7661 | 455.4777 | 0.4440 | Ceanothus |
| fixed | inoculum_site4 | -0.0589 | 0.9447 | -0.0623 | 453.7538 | 0.9503 | Ceanothus |
| fixed | inoculum_site5 | 0.1758 | 0.8327 | 0.2111 | 454.2433 | 0.8329 | Ceanothus |
| fixed | inoculum_site6 | -1.2336 | 1.0233 | -1.2054 | 455.5683 | 0.2287 | Ceanothus |
| fixed | inoculum_siteSterile | 1.8420 | 1.2874 | 1.4308 | 456.2794 | 0.1532 | Ceanothus |
| fixed | proportion_pathogen:droughtND | 4.3306 | 3.1467 | 1.3762 | 455.0446 | 0.1694 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site2 | 1.8041 | 2.0727 | 0.8704 | 455.4317 | 0.3845 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site3 | 1.9558 | 3.8777 | 0.5044 | 455.7795 | 0.6142 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site4 | 1.8027 | 2.5595 | 0.7043 | 453.5567 | 0.4816 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site5 | 1.2158 | 2.6144 | 0.4651 | 454.3078 | 0.6421 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site6 | 4.3705 | 2.8962 | 1.5091 | 455.6029 | 0.1320 | Ceanothus |
| fixed | proportion_pathogen:inoculum_siteSterile | -4.5708 | 3.7119 | -1.2314 | 456.4273 | 0.2188 | Ceanothus |
| fixed | droughtND:inoculum_site2 | 2.0379 | 1.1867 | 1.7173 | 454.9802 | 0.0866 | Ceanothus |
| fixed | droughtND:inoculum_site3 | 1.3625 | 1.4248 | 0.9563 | 457.1579 | 0.3394 | Ceanothus |
| fixed | droughtND:inoculum_site4 | 1.4098 | 1.3478 | 1.0460 | 455.1628 | 0.2961 | Ceanothus |
| fixed | droughtND:inoculum_site5 | 1.0741 | 1.4700 | 0.7307 | 456.8737 | 0.4653 | Ceanothus |
| fixed | droughtND:inoculum_site6 | 3.3012 | 1.3995 | 2.3588 | 454.9676 | 0.0188 | Ceanothus |
| fixed | droughtND:inoculum_siteSterile | 0.6023 | 1.7437 | 0.3454 | 453.9564 | 0.7299 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site2 | -7.0383 | 3.5798 | -1.9661 | 454.9522 | 0.0499 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site3 | -5.5899 | 4.8671 | -1.1485 | 457.3762 | 0.2514 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site4 | -3.9924 | 3.7044 | -1.0777 | 454.8204 | 0.2817 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site5 | -3.3364 | 4.7703 | -0.6994 | 456.9057 | 0.4847 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site6 | -10.2991 | 3.9875 | -2.5829 | 454.8270 | 0.0101 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_siteSterile | -2.7184 | 5.0102 | -0.5426 | 454.0323 | 0.5877 | Ceanothus |
| fixed | (Intercept) | -1.1684 | 0.6277 | -1.8615 | 278.4272 | 0.0637 | Abies |
| fixed | proportion_pathogen | 3.6405 | 1.9071 | 1.9089 | 548.7053 | 0.0568 | Abies |
| fixed | droughtND | 0.5966 | 0.7554 | 0.7898 | 549.6276 | 0.4300 | Abies |
| fixed | inoculum_site2 | 1.9585 | 0.8394 | 2.3331 | 548.2551 | 0.0200 | Abies |
| fixed | inoculum_site3 | 0.6020 | 0.7181 | 0.8383 | 547.3060 | 0.4022 | Abies |
| fixed | inoculum_site4 | 1.0022 | 0.7479 | 1.3400 | 547.1173 | 0.1808 | Abies |
| fixed | inoculum_site5 | 0.3777 | 0.9512 | 0.3971 | 546.8517 | 0.6915 | Abies |
| fixed | inoculum_site6 | -0.3107 | 0.8607 | -0.3609 | 549.1792 | 0.7183 | Abies |
| fixed | inoculum_siteSterile | 0.2462 | 0.9624 | 0.2558 | 549.5954 | 0.7982 | Abies |
| fixed | proportion_pathogen:droughtND | -2.1615 | 2.2353 | -0.9670 | 549.6902 | 0.3340 | Abies |
| fixed | proportion_pathogen:inoculum_site2 | -5.3043 | 2.6643 | -1.9909 | 548.3235 | 0.0470 | Abies |
| fixed | proportion_pathogen:inoculum_site3 | -3.4311 | 2.5609 | -1.3398 | 547.3609 | 0.1809 | Abies |
| fixed | proportion_pathogen:inoculum_site4 | -2.1426 | 2.5442 | -0.8421 | 547.1342 | 0.4001 | Abies |
| fixed | proportion_pathogen:inoculum_site5 | 1.9158 | 3.9387 | 0.4864 | 547.0462 | 0.6269 | Abies |
| fixed | proportion_pathogen:inoculum_site6 | 1.8835 | 2.9097 | 0.6473 | 549.2818 | 0.5177 | Abies |
| fixed | proportion_pathogen:inoculum_siteSterile | -2.1258 | 3.0883 | -0.6884 | 549.6680 | 0.4915 | Abies |
| fixed | droughtND:inoculum_site2 | -0.3348 | 1.2451 | -0.2689 | 547.5612 | 0.7881 | Abies |
| fixed | droughtND:inoculum_site3 | -0.5237 | 1.0952 | -0.4782 | 551.4256 | 0.6327 | Abies |
| fixed | droughtND:inoculum_site4 | 0.8235 | 0.9415 | 0.8747 | 546.9998 | 0.3821 | Abies |
| fixed | droughtND:inoculum_site5 | -0.0074 | 1.1616 | -0.0063 | 547.6782 | 0.9949 | Abies |
| fixed | droughtND:inoculum_site6 | 0.7503 | 1.3710 | 0.5472 | 548.5841 | 0.5844 | Abies |
| fixed | droughtND:inoculum_siteSterile | 0.3780 | 1.4953 | 0.2528 | 549.3380 | 0.8005 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site2 | 1.2884 | 3.6496 | 0.3530 | 547.6652 | 0.7242 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site3 | 1.4331 | 3.7849 | 0.3786 | 550.3306 | 0.7051 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site4 | -0.0528 | 3.1301 | -0.0169 | 547.1331 | 0.9866 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site5 | -1.9470 | 4.3400 | -0.4486 | 547.4146 | 0.6539 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site6 | -2.6534 | 4.1681 | -0.6366 | 548.8049 | 0.5247 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_siteSterile | -0.1118 | 4.4805 | -0.0250 | 549.3584 | 0.9801 | Abies |
Fungi
How does the proportion of mutualist fungi relate to indicators of plant health?
In the following figure, the X-axis represents the proportion of fungi that could be identified to a mutualistic guild; the Y-axis represents the value of the various measures of plant success (facets). Y-axis scales vary between facets.
We see an opposite pattern when looking at the proportions of putatively pathogenic fungi
| effect | term | estimate | std.error | statistic | df | p.value | species |
|---|---|---|---|---|---|---|---|
| fixed | (Intercept) | -0.6206 | 0.2539 | -2.4437 | 55.1101 | 0.0178 | Ceanothus |
| fixed | proportion_pathogen | 0.0054 | 1.5614 | 0.0035 | 457.7107 | 0.9972 | Ceanothus |
| fixed | droughtND | 0.8428 | 0.2734 | 3.0830 | 455.9070 | 0.0022 | Ceanothus |
| fixed | inoculum_site2 | 0.3041 | 0.2835 | 1.0727 | 457.0738 | 0.2840 | Ceanothus |
| fixed | inoculum_site3 | 0.1344 | 0.2990 | 0.4496 | 457.2861 | 0.6532 | Ceanothus |
| fixed | inoculum_site4 | 0.3135 | 0.2792 | 1.1230 | 455.4997 | 0.2620 | Ceanothus |
| fixed | inoculum_site5 | 0.5478 | 0.2922 | 1.8745 | 454.2481 | 0.0615 | Ceanothus |
| fixed | inoculum_site6 | 0.5105 | 0.4132 | 1.2354 | 457.6179 | 0.2173 | Ceanothus |
| fixed | inoculum_siteSterile | 0.6209 | 0.3546 | 1.7512 | 455.3257 | 0.0806 | Ceanothus |
| fixed | proportion_pathogen:droughtND | 0.1774 | 1.7416 | 0.1018 | 457.7728 | 0.9189 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site2 | 0.5303 | 1.9913 | 0.2663 | 457.9753 | 0.7901 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site3 | -2.1050 | 1.9835 | -1.0613 | 457.9997 | 0.2891 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site4 | 1.1373 | 1.9865 | 0.5725 | 456.9036 | 0.5673 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site5 | -0.0184 | 1.6735 | -0.0110 | 456.0497 | 0.9912 | Ceanothus |
| fixed | proportion_pathogen:inoculum_site6 | -1.7846 | 2.6850 | -0.6647 | 457.9989 | 0.5066 | Ceanothus |
| fixed | proportion_pathogen:inoculum_siteSterile | -2.9619 | 2.0318 | -1.4578 | 456.4852 | 0.1456 | Ceanothus |
| fixed | droughtND:inoculum_site2 | 0.0832 | 0.3752 | 0.2217 | 457.0510 | 0.8247 | Ceanothus |
| fixed | droughtND:inoculum_site3 | -0.9731 | 0.3917 | -2.4845 | 457.1136 | 0.0133 | Ceanothus |
| fixed | droughtND:inoculum_site4 | 0.3713 | 0.3656 | 1.0157 | 455.2958 | 0.3103 | Ceanothus |
| fixed | droughtND:inoculum_site5 | 0.0142 | 0.3787 | 0.0376 | 455.0280 | 0.9700 | Ceanothus |
| fixed | droughtND:inoculum_site6 | -0.3019 | 0.4833 | -0.6246 | 457.6711 | 0.5325 | Ceanothus |
| fixed | droughtND:inoculum_siteSterile | -0.6398 | 0.4347 | -1.4717 | 455.0357 | 0.1418 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site2 | 4.8521 | 5.9000 | 0.8224 | 457.9850 | 0.4113 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site3 | 2.6732 | 2.1909 | 1.2201 | 457.9916 | 0.2230 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site4 | -6.0638 | 6.3317 | -0.9577 | 457.6471 | 0.3387 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site5 | 0.2554 | 4.0843 | 0.0625 | 457.7288 | 0.9502 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_site6 | 0.1759 | 3.4237 | 0.0514 | 457.5146 | 0.9590 | Ceanothus |
| fixed | proportion_pathogen:droughtND:inoculum_siteSterile | 1.8355 | 4.7671 | 0.3850 | 457.9841 | 0.7004 | Ceanothus |
| fixed | (Intercept) | 0.1478 | 0.2478 | 0.5964 | 13.8739 | 0.5605 | Abies |
| fixed | proportion_pathogen | -1.9751 | 0.9250 | -2.1354 | 548.8206 | 0.0332 | Abies |
| fixed | droughtND | 0.0247 | 0.2145 | 0.1154 | 547.9589 | 0.9082 | Abies |
| fixed | inoculum_site2 | 0.0796 | 0.2039 | 0.3901 | 547.6619 | 0.6966 | Abies |
| fixed | inoculum_site3 | -0.7450 | 0.2235 | -3.3342 | 547.9680 | 0.0009 | Abies |
| fixed | inoculum_site4 | 0.2825 | 0.1956 | 1.4440 | 546.2481 | 0.1493 | Abies |
| fixed | inoculum_site5 | 0.3839 | 0.2171 | 1.7683 | 547.0385 | 0.0776 | Abies |
| fixed | inoculum_site6 | -0.0544 | 0.2123 | -0.2563 | 547.8979 | 0.7978 | Abies |
| fixed | inoculum_siteSterile | -0.5612 | 0.1991 | -2.8189 | 546.2514 | 0.0050 | Abies |
| fixed | proportion_pathogen:droughtND | 0.9260 | 1.1581 | 0.7995 | 549.7808 | 0.4243 | Abies |
| fixed | proportion_pathogen:inoculum_site2 | 4.1635 | 3.4089 | 1.2214 | 549.5705 | 0.2225 | Abies |
| fixed | proportion_pathogen:inoculum_site3 | 2.6887 | 1.3328 | 2.0173 | 549.5680 | 0.0441 | Abies |
| fixed | proportion_pathogen:inoculum_site4 | -5.2127 | 2.3490 | -2.2191 | 546.9085 | 0.0269 | Abies |
| fixed | proportion_pathogen:inoculum_site5 | 1.4309 | 1.0617 | 1.3477 | 548.3326 | 0.1783 | Abies |
| fixed | proportion_pathogen:inoculum_site6 | 1.7646 | 1.1940 | 1.4779 | 549.8710 | 0.1400 | Abies |
| fixed | proportion_pathogen:inoculum_siteSterile | 1.8120 | 0.9748 | 1.8588 | 547.3155 | 0.0636 | Abies |
| fixed | droughtND:inoculum_site2 | -0.1984 | 0.2886 | -0.6874 | 548.2016 | 0.4921 | Abies |
| fixed | droughtND:inoculum_site3 | -0.1630 | 0.3276 | -0.4976 | 550.8398 | 0.6190 | Abies |
| fixed | droughtND:inoculum_site4 | 0.3025 | 0.2972 | 1.0176 | 546.9898 | 0.3093 | Abies |
| fixed | droughtND:inoculum_site5 | -0.4240 | 0.2957 | -1.4337 | 547.2791 | 0.1522 | Abies |
| fixed | droughtND:inoculum_site6 | -0.0196 | 0.2954 | -0.0662 | 548.2796 | 0.9472 | Abies |
| fixed | droughtND:inoculum_siteSterile | 0.4723 | 0.2999 | 1.5750 | 547.4331 | 0.1158 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site2 | -2.0132 | 3.5833 | -0.5618 | 550.2289 | 0.5745 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site3 | -0.8609 | 1.7701 | -0.4863 | 551.5755 | 0.6269 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site4 | 83.6612 | 27.2828 | 3.0664 | 548.5544 | 0.0023 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site5 | 3.2732 | 1.9160 | 1.7083 | 548.7870 | 0.0881 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_site6 | -0.4152 | 1.5803 | -0.2627 | 550.2599 | 0.7929 | Abies |
| fixed | proportion_pathogen:droughtND:inoculum_siteSterile | -5.4061 | 2.1744 | -2.4862 | 549.0231 | 0.0132 | Abies |
| fixed | (Intercept) | -0.8022 | 0.3399 | -2.3599 | 161.0649 | 0.0195 | Ceanothus |
| fixed | proportion_mutualist | 0.3218 | 0.5106 | 0.6302 | 457.5517 | 0.5289 | Ceanothus |
| fixed | droughtND | 0.6591 | 0.4237 | 1.5554 | 456.3827 | 0.1205 | Ceanothus |
| fixed | inoculum_site2 | 0.3828 | 0.3705 | 1.0332 | 456.4647 | 0.3021 | Ceanothus |
| fixed | inoculum_site3 | -0.4801 | 0.3963 | -1.2115 | 456.6666 | 0.2263 | Ceanothus |
| fixed | inoculum_site4 | 0.9985 | 0.6939 | 1.4390 | 457.2532 | 0.1508 | Ceanothus |
| fixed | inoculum_site5 | 0.6621 | 0.3773 | 1.7547 | 457.9637 | 0.0800 | Ceanothus |
| fixed | inoculum_site6 | 0.2690 | 0.3783 | 0.7111 | 455.7693 | 0.4774 | Ceanothus |
| fixed | inoculum_siteSterile | -0.7110 | 0.8686 | -0.8186 | 456.9198 | 0.4135 | Ceanothus |
| fixed | proportion_mutualist:droughtND | 0.9691 | 0.9799 | 0.9890 | 457.2576 | 0.3232 | Ceanothus |
| fixed | proportion_mutualist:inoculum_site2 | 0.7436 | 1.1344 | 0.6555 | 457.6023 | 0.5125 | Ceanothus |
| fixed | proportion_mutualist:inoculum_site3 | 0.8005 | 0.6597 | 1.2134 | 457.3896 | 0.2256 | Ceanothus |
| fixed | proportion_mutualist:inoculum_site4 | -1.3078 | 1.5481 | -0.8448 | 457.4213 | 0.3987 | Ceanothus |
| fixed | proportion_mutualist:inoculum_site5 | 0.3756 | 1.6375 | 0.2294 | 457.8880 | 0.8187 | Ceanothus |
| fixed | proportion_mutualist:inoculum_site6 | 1.0091 | 1.4034 | 0.7190 | 457.2809 | 0.4725 | Ceanothus |
| fixed | proportion_mutualist:inoculum_siteSterile | 1.6008 | 1.6381 | 0.9772 | 457.0660 | 0.3290 | Ceanothus |
| fixed | droughtND:inoculum_site2 | 0.3825 | 0.5067 | 0.7549 | 457.2408 | 0.4507 | Ceanothus |
| fixed | droughtND:inoculum_site3 | 0.0189 | 0.5346 | 0.0354 | 457.3001 | 0.9718 | Ceanothus |
| fixed | droughtND:inoculum_site4 | -0.7769 | 0.8372 | -0.9280 | 456.4201 | 0.3539 | Ceanothus |
| fixed | droughtND:inoculum_site5 | 0.4308 | 0.5170 | 0.8333 | 457.4848 | 0.4051 | Ceanothus |
| fixed | droughtND:inoculum_site6 | -0.5954 | 0.5138 | -1.1587 | 457.4218 | 0.2472 | Ceanothus |
| fixed | droughtND:inoculum_siteSterile | 1.0775 | 1.0150 | 1.0616 | 455.7404 | 0.2890 | Ceanothus |
| fixed | proportion_mutualist:droughtND:inoculum_site2 | -1.4437 | 1.6302 | -0.8856 | 457.9597 | 0.3763 | Ceanothus |
| fixed | proportion_mutualist:droughtND:inoculum_site3 | -1.6146 | 1.1588 | -1.3933 | 457.9576 | 0.1642 | Ceanothus |
| fixed | proportion_mutualist:droughtND:inoculum_site4 | 1.0803 | 1.8058 | 0.5982 | 455.7461 | 0.5500 | Ceanothus |
| fixed | proportion_mutualist:droughtND:inoculum_site5 | -2.1865 | 1.9014 | -1.1499 | 457.7228 | 0.2508 | Ceanothus |
| fixed | proportion_mutualist:droughtND:inoculum_site6 | 2.9041 | 1.8986 | 1.5296 | 456.9243 | 0.1268 | Ceanothus |
| fixed | proportion_mutualist:droughtND:inoculum_siteSterile | -2.9672 | 1.9533 | -1.5191 | 457.0488 | 0.1294 | Ceanothus |
| fixed | (Intercept) | -0.5757 | 0.3669 | -1.5690 | 62.0891 | 0.1217 | Abies |
| fixed | proportion_mutualist | 0.6794 | 0.4248 | 1.5995 | 549.1340 | 0.1103 | Abies |
| fixed | droughtND | -0.0667 | 0.4641 | -0.1437 | 549.0047 | 0.8858 | Abies |
| fixed | inoculum_site2 | 0.8297 | 0.4183 | 1.9837 | 548.5466 | 0.0478 | Abies |
| fixed | inoculum_site3 | -0.0018 | 0.3381 | -0.0053 | 548.3096 | 0.9958 | Abies |
| fixed | inoculum_site4 | 0.3730 | 0.4131 | 0.9029 | 547.3019 | 0.3670 | Abies |
| fixed | inoculum_site5 | 1.2056 | 0.3598 | 3.3509 | 547.8740 | 0.0009 | Abies |
| fixed | inoculum_site6 | 0.3313 | 0.3982 | 0.8319 | 547.6122 | 0.4058 | Abies |
| fixed | inoculum_siteSterile | -0.3805 | 0.3705 | -1.0268 | 548.1281 | 0.3050 | Abies |
| fixed | proportion_mutualist:droughtND | 0.1357 | 0.6173 | 0.2198 | 549.3408 | 0.8261 | Abies |
| fixed | proportion_mutualist:inoculum_site2 | -0.7573 | 0.6259 | -1.2100 | 548.8757 | 0.2268 | Abies |
| fixed | proportion_mutualist:inoculum_site3 | -0.6754 | 0.6565 | -1.0287 | 548.4715 | 0.3041 | Abies |
| fixed | proportion_mutualist:inoculum_site4 | -0.1363 | 0.5557 | -0.2453 | 547.3979 | 0.8063 | Abies |
| fixed | proportion_mutualist:inoculum_site5 | -2.6207 | 1.1763 | -2.2280 | 548.2486 | 0.0263 | Abies |
| fixed | proportion_mutualist:inoculum_site6 | -0.0784 | 0.7127 | -0.1100 | 547.8722 | 0.9125 | Abies |
| fixed | proportion_mutualist:inoculum_siteSterile | 0.2307 | 0.5512 | 0.4186 | 548.2973 | 0.6757 | Abies |
| fixed | droughtND:inoculum_site2 | 0.4104 | 0.5680 | 0.7226 | 547.7570 | 0.4702 | Abies |
| fixed | droughtND:inoculum_site3 | -0.2531 | 0.5176 | -0.4891 | 551.7549 | 0.6250 | Abies |
| fixed | droughtND:inoculum_site4 | 3.4378 | 0.9621 | 3.5732 | 549.2918 | 0.0004 | Abies |
| fixed | droughtND:inoculum_site5 | -0.4996 | 0.5684 | -0.8791 | 547.4239 | 0.3797 | Abies |
| fixed | droughtND:inoculum_site6 | 0.4695 | 0.5484 | 0.8561 | 548.0989 | 0.3923 | Abies |
| fixed | droughtND:inoculum_siteSterile | 0.7380 | 0.5395 | 1.3680 | 548.5313 | 0.1719 | Abies |
| fixed | proportion_mutualist:droughtND:inoculum_site2 | -1.0961 | 0.8196 | -1.3373 | 548.0729 | 0.1817 | Abies |
| fixed | proportion_mutualist:droughtND:inoculum_site3 | 0.8786 | 1.0742 | 0.8180 | 206.1281 | 0.4143 | Abies |
| fixed | proportion_mutualist:droughtND:inoculum_site4 | -3.2430 | 1.1791 | -2.7503 | 549.2426 | 0.0062 | Abies |
| fixed | proportion_mutualist:droughtND:inoculum_site5 | 2.0835 | 1.3407 | 1.5540 | 547.9146 | 0.1208 | Abies |
| fixed | proportion_mutualist:droughtND:inoculum_site6 | -1.0679 | 0.8860 | -1.2053 | 547.7981 | 0.2286 | Abies |
| fixed | proportion_mutualist:droughtND:inoculum_siteSterile | -0.9759 | 0.9337 | -1.0452 | 548.9449 | 0.2964 | Abies |
Beta-Diversity
Bacteria
## PermANOVA run without outlier Sterile-inoculum root samples...| term | df | SumOfSqs | R2 | statistic | p.value |
|---|---|---|---|---|---|
| host | 1 | 3.8414120 | 0.0687480 | 11.063965 | 0.001 |
| fire_freq | 1 | 1.7434756 | 0.0312022 | 5.021527 | 0.001 |
| drought | 1 | 0.8088162 | 0.0144750 | 2.329538 | 0.001 |
| host:fire_freq | 1 | 0.7153777 | 0.0128028 | 2.060418 | 0.002 |
| host:drought | 1 | 0.7562988 | 0.0135351 | 2.178278 | 0.002 |
| fire_freq:drought | 1 | 0.3814427 | 0.0068265 | 1.098624 | 0.234 |
| host:fire_freq:drought | 1 | 0.4106606 | 0.0073494 | 1.182777 | 0.162 |
| Residual | 136 | 47.2192419 | 0.8450610 | NA | NA |
| Total | 143 | 55.8767255 | 1.0000000 | NA | NA |
Fungi
## PermANOVA run without outlier Sterile-inoculum root samples...| term | df | SumOfSqs | R2 | statistic | p.value |
|---|---|---|---|---|---|
| host | 1 | 1.9352113 | 0.0300393 | 4.6753844 | 0.001 |
| fire_freq | 1 | 3.4231420 | 0.0531356 | 8.2701587 | 0.001 |
| drought | 1 | 0.5712680 | 0.0088675 | 1.3801580 | 0.113 |
| host:fire_freq | 1 | 0.9705051 | 0.0150646 | 2.3446971 | 0.003 |
| host:drought | 1 | 0.3803731 | 0.0059043 | 0.9189645 | 0.583 |
| fire_freq:drought | 1 | 0.5128794 | 0.0079612 | 1.2390938 | 0.202 |
| host:fire_freq:drought | 1 | 0.3369443 | 0.0052302 | 0.8140424 | 0.746 |
| Residual | 136 | 56.2924276 | 0.8737973 | NA | NA |
| Total | 143 | 64.4227507 | 1.0000000 | NA | NA |
AMF
## PermANOVA run without outlier Sterile-inoculum root samples...| term | df | SumOfSqs | R2 | statistic | p.value |
|---|---|---|---|---|---|
| inoculum_site | 6 | 6.9907731 | 0.2129210 | 2.9819777 | 0.001 |
| drought | 1 | 0.3007071 | 0.0091588 | 0.7696159 | 0.783 |
| inoculum_site:drought | 6 | 2.0978089 | 0.0638939 | 0.8948394 | 0.794 |
| Residual | 60 | 23.4434120 | 0.7140263 | NA | NA |
| Total | 73 | 32.8327011 | 1.0000000 | NA | NA |
Important Taxa
These taxa were identified by both Random Forest models and corncob as being important predictors of the various experimental conditions & had significant differential abundance between levels of those variables
Bacteria
Differential Abundance
Relative Abundances of ‘important’ taxa in root samples
Fungi
Differential Abundance
No fungal taxa were found to have significant differential abundance between drought levels
Relative Abundances of ‘important’ taxa in root samples
AMF
Differential Abundance
No fungal taxa were found to have significant differential abundance between drought levels
Relative Abundances of ‘important’ taxa in root samples
Phylogenetic properties
Bacteria
- Still kind of messy
- What specific questions do we need to address with this?
Fungi
- Phylogenetic dispersion is tricky with ITS markers :(
- Could try GhostTree for fungi of interest that come up as ‘unknown’
Network properties
Selected network attributes
Network properties vs Plant Health
(Composite scaled-centered plant health measures)
## plant_health_indicator ~ species * kingdom * (n_vertices + n_edges +
## mean_dist + mean_betweenness + mean_closeness + global_effic +
## clustering_coeficient + max_degree)| term | estimate | std.error | statistic | p.value |
|---|---|---|---|---|
| (Intercept) | -0.3395498 | 1.1487865 | -0.2955726 | 0.7675797 |
| speciesSnowbrush | 0.7900657 | 1.0513415 | 0.7514834 | 0.4524286 |
| kingdomBacteria | 0.7824899 | 1.1780848 | 0.6642051 | 0.5066169 |
| kingdomFungi | -0.1216436 | 0.9017750 | -0.1348935 | 0.8927063 |
| n_vertices | 0.0336583 | 0.0182490 | 1.8443884 | 0.0652382 |
| n_edges | -0.0062740 | 0.0025937 | -2.4189740 | 0.0156314 |
| mean_dist | 0.1045359 | 0.2745054 | 0.3808154 | 0.7033708 |
| mean_betweenness | -0.0093545 | 0.0130007 | -0.7195376 | 0.4718733 |
| mean_closeness | -0.4507788 | 1.6083510 | -0.2802739 | 0.7792893 |
| global_effic | 0.0709782 | 0.8650863 | 0.0820475 | 0.9346151 |
| clustering_coeficient | 0.5004481 | 0.2923773 | 1.7116517 | 0.0870780 |
| max_degree | -0.0027581 | 0.0111646 | -0.2470390 | 0.8048972 |
| speciesSnowbrush:kingdomBacteria | -1.9196549 | 1.3356853 | -1.4372060 | 0.1507777 |
| speciesSnowbrush:kingdomFungi | NA | NA | NA | NA |
| speciesSnowbrush:n_vertices | -0.0277443 | 0.0162003 | -1.7125829 | 0.0869064 |
| speciesSnowbrush:n_edges | 0.0056234 | 0.0022927 | 2.4526859 | 0.0142435 |
| speciesSnowbrush:mean_dist | -0.1783225 | 0.2516005 | -0.7087527 | 0.4785404 |
| speciesSnowbrush:mean_betweenness | 0.0069343 | 0.0117019 | 0.5925841 | 0.5535102 |
| speciesSnowbrush:mean_closeness | 0.0505584 | 1.5604034 | 0.0324008 | 0.9741548 |
| speciesSnowbrush:global_effic | -0.2616951 | 0.7889638 | -0.3316946 | 0.7401461 |
| speciesSnowbrush:clustering_coeficient | -0.4328359 | 0.2784180 | -1.5546258 | 0.1201548 |
| speciesSnowbrush:max_degree | 0.0010310 | 0.0103857 | 0.0992750 | 0.9209275 |
| kingdomBacteria:n_vertices | -0.0412751 | 0.0191732 | -2.1527432 | 0.0314290 |
| kingdomFungi:n_vertices | -0.0131249 | 0.0107850 | -1.2169553 | 0.2237297 |
| kingdomBacteria:n_edges | 0.0070137 | 0.0038534 | 1.8201147 | 0.0688544 |
| kingdomFungi:n_edges | 0.0016993 | 0.0014452 | 1.1758683 | 0.2397532 |
| kingdomBacteria:mean_dist | -0.1393771 | 0.2812262 | -0.4956049 | 0.6202143 |
| kingdomFungi:mean_dist | 0.0793556 | 0.2149002 | 0.3692673 | 0.7119580 |
| kingdomBacteria:mean_betweenness | 0.0127671 | 0.0132366 | 0.9645311 | 0.3348678 |
| kingdomFungi:mean_betweenness | 0.0051542 | 0.0075743 | 0.6804893 | 0.4962542 |
| kingdomBacteria:mean_closeness | 0.2616321 | 1.6248329 | 0.1610209 | 0.8720892 |
| kingdomFungi:mean_closeness | 0.8705704 | 1.2202795 | 0.7134189 | 0.4756495 |
| kingdomBacteria:global_effic | -0.5859759 | 0.9583746 | -0.6114268 | 0.5409696 |
| kingdomFungi:global_effic | 0.1112992 | 0.6967625 | 0.1597377 | 0.8730999 |
| kingdomBacteria:clustering_coeficient | -0.0612045 | 0.3475835 | -0.1760857 | 0.8602401 |
| kingdomFungi:clustering_coeficient | -0.3444858 | 0.2348469 | -1.4668530 | 0.1425348 |
| kingdomBacteria:max_degree | 0.0169423 | 0.0144749 | 1.1704638 | 0.2419197 |
| kingdomFungi:max_degree | 0.0104688 | 0.0062428 | 1.6769499 | 0.0936703 |
| speciesSnowbrush:kingdomBacteria:n_vertices | 0.0342394 | 0.0190432 | 1.7979889 | 0.0722927 |
| speciesSnowbrush:kingdomFungi:n_vertices | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:n_edges | -0.0036401 | 0.0041559 | -0.8758998 | 0.3811640 |
| speciesSnowbrush:kingdomFungi:n_edges | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:mean_dist | 0.4252445 | 0.2905229 | 1.4637210 | 0.1433889 |
| speciesSnowbrush:kingdomFungi:mean_dist | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:mean_betweenness | -0.0169793 | 0.0126385 | -1.3434610 | 0.1792379 |
| speciesSnowbrush:kingdomFungi:mean_betweenness | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:mean_closeness | 2.0054281 | 1.7097727 | 1.1729209 | 0.2409331 |
| speciesSnowbrush:kingdomFungi:mean_closeness | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:global_effic | 2.4227245 | 1.3447266 | 1.8016483 | 0.0717145 |
| speciesSnowbrush:kingdomFungi:global_effic | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:clustering_coeficient | -0.6159688 | 0.4870200 | -1.2647710 | 0.2060648 |
| speciesSnowbrush:kingdomFungi:clustering_coeficient | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:max_degree | -0.0157006 | 0.0160879 | -0.9759266 | 0.3291900 |
| speciesSnowbrush:kingdomFungi:max_degree | NA | NA | NA | NA |
_____
Soil chemistry
Overview of soil properties for each inoculum source:
Testing for significant differences between the samples…
Here are the soil properties that differ significantly between inoculum sources. Sterile inoculum soils are set as the intercept. The stats below pretty nicely reflect the obvious patterns in the overall figure.| term | estimate | std.error | statistic | p.value |
|---|---|---|---|---|
| Mn | 1.248 | 0.268 | 4.658 | 0.000 |
| NH4 | 0.770 | 0.268 | 2.875 | 0.004 |
| Fe:inoc_site1 | 1.516 | 0.328 | 4.618 | 0.000 |
| K:inoc_site1 | 0.904 | 0.328 | 2.753 | 0.006 |
| NO3:inoc_site1 | -0.793 | 0.328 | -2.417 | 0.016 |
| TKN:inoc_site1 | 0.735 | 0.328 | 2.240 | 0.026 |
| Zn:inoc_site1 | 1.160 | 0.328 | 3.536 | 0.000 |
| Fe:inoc_site2 | 0.831 | 0.328 | 2.532 | 0.012 |
| K:inoc_site2 | 0.801 | 0.328 | 2.440 | 0.015 |
| Mn:inoc_site2 | -1.081 | 0.328 | -3.294 | 0.001 |
| TKN:inoc_site2 | 0.660 | 0.328 | 2.010 | 0.045 |
| Mn:inoc_site3 | -1.526 | 0.328 | -4.648 | 0.000 |
| NH4:inoc_site3 | -0.976 | 0.328 | -2.973 | 0.003 |
| Zn:inoc_site3 | -0.693 | 0.328 | -2.112 | 0.035 |
| C:N:inoc_site4 | -0.893 | 0.328 | -2.721 | 0.007 |
| EC:inoc_site4 | -1.026 | 0.328 | -3.127 | 0.002 |
| Mn:inoc_site4 | -1.349 | 0.328 | -4.110 | 0.000 |
| B:inoc_site5 | 1.369 | 0.328 | 4.171 | 0.000 |
| Ca:inoc_site5 | 1.192 | 0.328 | 3.631 | 0.000 |
| K:inoc_site5 | 0.683 | 0.328 | 2.080 | 0.038 |
| Mg:inoc_site5 | 0.682 | 0.328 | 2.078 | 0.039 |
| Mn:inoc_site5 | -1.099 | 0.328 | -3.350 | 0.001 |
| NO3:inoc_site5 | 1.854 | 0.328 | 5.649 | 0.000 |
| TKN:inoc_site5 | 1.022 | 0.328 | 3.114 | 0.002 |
| Zn:inoc_site5 | 1.448 | 0.328 | 4.412 | 0.000 |
| B:inoc_site6 | 0.918 | 0.328 | 2.798 | 0.005 |
| Mn:inoc_site6 | -1.535 | 0.328 | -4.678 | 0.000 |
| NH4:inoc_site6 | -0.754 | 0.328 | -2.299 | 0.022 |
| NO3:inoc_site6 | 1.273 | 0.328 | 3.880 | 0.000 |
| Zn:inoc_site6 | 1.290 | 0.328 | 3.932 | 0.000 |